THE UTILITY OF atpBGENE SEQUENCES INRESOLVING PHYLOGENETICRELATIONSHIPS:COMPARISON WITH rbcLAND 18S RIBOSOMAL DNASEQUENCES IN THELARDIZABALACEAE'Sara B. Hoot,2 Alastair Culham,3 andPeter R. Crane4ABSTRACT The chloroplast gene atpB was sequenced for seven genera of the Lardizabalaceae and three outgroup taxa toassess its utility as a source of phylogenetic information. The resulting phylogenetic tree was compared with treesbased on 18S nuclear ribosomal DNA and rbcL (chloroplast DNA) sequences, as well as a combination of ail data(atpB, 18S, and rbcL) for the same taxa. Sequence divergence values, statistics related to patterns of charactertransformation, and indices measuring homoplasy and branch support were also compared. The topology of the treesderived from atpB, 18S, and a combination of ail three sequence data sets were largely congruent. Ail phylogenies,with the exception of the tree derived from rbcL data, supported the monophyly of the Lardizabalaceae. AU indicatorsof nucleotide substitution rate suggest that rbcL is the least conserved, atpB is intermediate, and 18S is the mostconserved of the three genes sequenced. Measures of homoplasy also indicate that the rbcL tree is less stronglysupported than those based on atpB, 18S, or a combination of atpB, 18S, and rbcL sequence data. Phylogenetic analyses of higher-level plantgroups using DNA sequence data have been basedmost often on the chloroplast gene rbcL or, lessfrequently, on 18S nuclear ribosomal DNA (18SnrDNA). Few phylogenetic studies have used othergene sequences across a broad range of taxa, andstill fewer have compared results from two or moregene sequences for the same taxa (e.g., Baldwin,1992; Johnson & Soltis, 1994; Olmstead & Sweere,1994). As part of an intensive systematic study ofphylogenetic relationships among basal eudicots(Ranunculidae and "lower" Hamamelididae), wehave further developed the chloroplast gene, atpB,as a new source of phylogenetically informativedata (Ritland & Clegg, 1987). Here, we apply theatpB gene to resolve phylogenetic relationships inthe angiosperm family Lardizabalaceae and com-pare the results with those based on rbcL and 18SnrDNA for the same taxa. Cladograms based onthe three genes are evaluated and compared interms of their resolution and congruence, as wellas various measures of phylogenetic signal, tran-sition/transversion bias, sequence divergence, andhomoplasy. Based on these data, we discuss theeffectiveness of using each gene for phylogeneticstudies at the generic level and above. The Lardizabalaceae (Ranunculidae, sensuTakhtajan, 1987-"ranunculids") are a family oftwining (rarely erect) shrubs found in temperateareas of Eastern Asia and South America. Thefamily is characterized by alternate, palmate (rare-ly pinnate) compound leaves; regular unisexualflowers; six overlapping or valvate sepals (three inAkebia); staminodia or petals small or absent; three ' We thank R. Olmstead and S. Lanyon for helpful comments on this manuscript, D. Nickrent and E. A. Zimmer for ribosomal DNA amplification and sequencing primers, and G. Zurawski for rbcL sequencing primers. We are grateful to the following for providing us with leaf material: R. McBeath, Royal Botanic Garden, Edinburgh; A. Reznicek, University of Michigan; T. Lammers, Field Museum of Natural History; M. Maunder and T. Upson, Royal Botanic Gardens, Kew; H. Qin, Chinese Academy of Sciences, Beijing; and E. van Jaarsveld, Kirstenbosch Botanical Garden. We also thank J. Hall for technical advice and A. Thurmond for laboratory assistance. This work was supported in part by NSF grants DEB-9020237 to PRC and DEB-9306533 to SBH. 1 Department of Biological Sciences, University of Wisconsin-Milwaukee, Lapham Hall, P.O. Box 413, Milwaukee,Wisconsin 53201, U.S.A. Department of Botany, School of Plant Sciences, University of Reading, Reading, RG6 2AS, U.K. * Departments of Botany and Geology, Field Museum, Chicago, Illinois 60605, U.S.A.ANN. MISSOURI BOT. GARD. 82: 194-207. 1995.